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(newest | oldest) View (newer 50 | older 50) (20 | 50 | 100 | 250 | 500)- 02:37, 10 May 2022 Root talk contribs created page Tinkergpu:Tinkercpu (Created page with " == Tinker CPU == For Tinker CPU code, download from github: [https://github.com/jayponder/tinker https://github.com/TinkerTools] (git clone recommended) Then follow the compilation instructions: [https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Poltype:Poltype#Notes_about_compiling_tinker_8_with_OpenMP https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Poltype:Poltype#Notes_about_compiling_tinker_8_with_OpenMP] You may also compile Tinker for...")
- 17:33, 7 May 2022 Root talk contribs created page File:Local frame.png
- 17:33, 7 May 2022 Root talk contribs uploaded File:Local frame.png
- 17:29, 7 May 2022 Root talk contribs deleted page File:Local frame.png
- 17:32, 22 April 2022 Root talk contribs created page ABS:Md tp (Created page with "== Ensemble== Typical microscopic ensembles * Microcanonical: <math>\; \Omega(E,V,N) = e^{S/k} </math> ** the probability density is proportional to <math>\delta = \aleph(q,p)-E\,</math> ---------------------- * Canonical: <math>\; Z(T,V,N) = e^{- \aleph/kT} </math> ** the probability density is proportional to <math> exp\left(-\frac{\aleph}{kT}\right)</math> --------------------------- * Grand canonical: <math>\; \Xi(T,V,\mu) = \sum_{N}^{}e^{(\mu N/kT)}{Z}_{NVT}...")
- 17:31, 22 April 2022 Root talk contribs created page ABS:Md integrator (Created page with "==Integrator== For numerical integration techniques, the book '''Numerical Recipes in C''' is good reference. As we already know MD simualtions is solving Newton's law <math>\frac{dU(x)}{dx}=m*\frac{d^2x}{dt^2}</math> using finite difference methods. The exact way to solve the ordinary differential equation depends on the integrator. A good integrator should allow *large time step (However, if the timestep is too large for system, the simulation can "blow up")...")
- 17:29, 22 April 2022 Root talk contribs created page ABS:Md erg (Created page with "==The Liouville equation== http://en.wikipedia.org/wiki/Liouville%27s_theorem_%28Hamiltonian%29#Liouville_equation Phase space distribution conserves over time as with the density of matter (mass conservation) Liousville eq describes the time evolution of phase space distribution function (hamiltonian describes individual member of the ensemble). Consider a dynamical system with canonical coordinates <math>q_i</math> and conjugate momenta <math>p_i</math>, where <mat...")
- 17:29, 22 April 2022 Root talk contribs created page ABS:Md ham (Created page with "Derivation of equation of motion from Lagrangian and Hamilton formulation of classical mechanics.<ref name="frenkel">Frenkel and Smit, Understanding Molecular Simulations From algorithm to Applications.</ref> <span style="font-size: larger;">The Hamiltonian and Lagrangian formulations of classical mechanics yield identical results. This is not surprising as the Hamiltonian formulation was derived from the Lagrangian equations (see section A.2). Yet, the forms of the Lag...")
- 16:36, 22 April 2022 Root talk contribs created page ABS:Mm aplus (Created page with "=Charge Penetration= http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00267")
- 16:35, 22 April 2022 Root talk contribs created page ABS:Mm CP (Created page with "http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00267")
- 16:35, 22 April 2022 Root talk contribs created page ABS:Mm ewald (Created page with "==Truncation of long-range interaction== For condense-phase simualtion, Periodic Boundary Conditon is used to avoid the boundary effect. 480px It is expensive to compute all pairs of interactions. Solution: cutoff? Longer cutoff is (may be) more accurate but more expensive. 480px ==Electrostatics== Electrostatic interactions die off very slowly. In crystal the interaction can be rather long-ranged. '''Cutoff is a bad idea.'...")
- 16:34, 22 April 2022 Root talk contribs created page ABS:Mm mpole (Created page with "== Is electrostatic important? == '''All forces are electrostatic in nature.''' 399px == Buckingham, Advances in Chemical Physics, 12, 107-142 (1967) == https://doi.org/10.1002/9780470143582.ch2 There is now general agreement that the significant forces between atoms and molecules have an electric origin. It is true that other sources exist, such as magnetic and gravitational interactions, but these can normally be neglected. When the molecule...")
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:5 9 2014 lipid bilayer indolicidin.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:5 9 2014 lipid bilayer indolicidin.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Rna energy optimization.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Rna energy optimization.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Start diffusion simulations.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Start diffusion simulations.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Qd presentation 9 5.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Qd presentation 9 5.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Harger10 10paper.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Harger10 10paper.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Rna therapeutics.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Rna therapeutics.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:RenGroupMeeting 07 31 15 sara final.pptx.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:RenGroupMeeting 07 31 15 sara final.pptx.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Stone-SAPT-Polarizability.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Stone-SAPT-Polarizability.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Connolly.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Connolly.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:02 20 15 BME presentation sara.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:02 20 15 BME presentation sara.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Lee-richards71.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Lee-richards71.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Proposal ZhifengJing Apr2018.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Proposal ZhifengJing Apr2018.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Sanner96.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Sanner96.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Group Meeting Sep.11th Chengwen.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Group Meeting Sep.11th Chengwen.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Mukherjee2008.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Mukherjee2008.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Poisson-Boltzmann Methods for Biomolecular Electrostatics-Baker.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Poisson-Boltzmann Methods for Biomolecular Electrostatics-Baker.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:OSRW-5 2 2011.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:OSRW-5 2 2011.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Server room 2016 Sept.pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Server room 2016 Sept.pdf (== Summary == Importing file) Tag: Server-side upload
- 16:29, 22 April 2022 Maintenance script talk contribs created page File:Pande - PNAS (2009).pdf (== Summary == Importing file)
- 16:29, 22 April 2022 Maintenance script talk contribs uploaded File:Pande - PNAS (2009).pdf (== Summary == Importing file) Tag: Server-side upload
